I'm having a problem with the following command:
fastq-dump --split-files --origfmt SRR1611183
Here is the error message:
2018-03-06T01:50:18 fastq-dump.2.3.5 err: error unexpected while resolving tree within virtual file system module - failed to resolve accession 'SRR1611183' - Obsolete software. See https://github.com/ncbi/sra-tools/wiki ( 406 ) Redirected!!! 2018-03-06T01:50:18 fastq-dump.2.3.5 err: name incorrect while evaluating path within network system module - Scheme is 'https' 2018-03-06T01:50:18 fastq-dump.2.3.5 err: item not found while constructing within virtual database module - the path 'SRR1611183' cannot be opened as database or table
I've researched the issue on the web and the consensus was that I needed to update my sra toolkit to the latest version 2.9.0 (so I did); however, I'm still getting the same error message?
Some more troubleshooting, I type in the following:
$ which fastq-dump
Then I try a test from the github instructions:
fastq-dump --stdout SRR390728 | head -n 8
and get the same error...
I guess I could just download the data directly from EMBL-EBI (https://www.ebi.ac.uk/ena/data/view/SRR1611183) but I really want to figure this one out.